From d61356dfeaaa4e2e7f0b0a58875a90da67aa210c Mon Sep 17 00:00:00 2001 From: Anne Fouilloux Date: Fri, 9 Dec 2016 12:18:18 +0100 Subject: [PATCH] changed ipython to jupyter When converting jupyter notebook to html, ipython command is used instead of jupyter (ipython is becoming obsolete). --- config/galaxy.ini.sample | 2 +- lib/galaxy/datatypes/text.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index a50baf8afb7..972c9d6735e 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -784,7 +784,7 @@ nglims_config_file = tool-data/nglims.yaml # notebooks in Galaxy histories. This process may allow users to execute # arbitrary code or serve arbitrary HTML. If enabled, IPython must be # available and on Galaxy's PATH, to do this run -# `pip install jinja2 pygments ipython` in Galaxy's virtualenv. +# `pip install jinja2 pygments jupyter` in Galaxy's virtualenv. #trust_ipython_notebook_conversion = False # Debug enables access to various config options useful for development and diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py index a1dc9388d65..dcb54c0cd0e 100644 --- a/lib/galaxy/datatypes/text.py +++ b/lib/galaxy/datatypes/text.py @@ -144,7 +144,7 @@ class Ipynb( Json ): ofilename = ofile_handle.name ofile_handle.close() try: - cmd = 'ipython nbconvert --to html --template full %s --output %s' % (dataset.file_name, ofilename) + cmd = 'jupyter nbconvert --to html --template full %s --output %s' % (dataset.file_name, ofilename) log.info("Calling command %s" % cmd) subprocess.call(cmd, shell=True) ofilename = '%s.html' % ofilename